Package: mummer Version: 3.23+dfsg-4 Severity: important Hello everybody,
the `mummerplot` Perl script in the mummer package is broken because it contains some deprecated Perl syntax. The attached patch solves the problem. I am not sure if it is enough for a Stable update. In Sid, maybe it is a sign that an upgrade to MUMmer4 (where at least this issue is fixed) would be useful. Have a nice day, Charles -- System Information: Debian Release: 10.3 APT prefers stable APT policy: (900, 'stable'), (500, 'stable-updates') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.19.0-8-amd64 (SMP w/4 CPU cores) Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8), LANGUAGE=fr_FR.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages mummer depends on: ii gawk 1:4.2.1+dfsg-1 ii libc6 2.28-10 ii libgcc1 1:8.3.0-6 ii libstdc++6 8.3.0-6 ii perl 5.28.1-6 mummer recommends no packages. mummer suggests no packages. -- no debconf information
--- /usr/bin/mummerplot 2018-06-11 15:38:49.000000000 +0900 +++ mummerplot.patched 2020-04-15 13:38:35.483544650 +0900 @@ -881,7 +881,7 @@ my ($refoff, $reflen, $refdir); my ($qryoff, $qrylen, $qrydir); - if ( defined (%$rref) ) { + if ( %$rref ) { #-- skip reference sequence or set atts from hash if ( !exists ($rref->{$idR}) ) { next; } else { ($refoff, $reflen, $refdir) = @{$rref->{$idR}}; } @@ -891,7 +891,7 @@ ($refoff, $reflen, $refdir) = (0, $lenR, 1); } - if ( defined (%$qref) ) { + if ( %$qref ) { #-- skip query sequence or set atts from hash if ( !exists ($qref->{$idQ}) ) { next; } else { ($qryoff, $qrylen, $qrydir) = @{$qref->{$idQ}}; } @@ -978,7 +978,7 @@ my ($refoff, $reflen, $refdir); my ($qryoff, $qrylen, $qrydir); - if ( defined (%$rref) ) { + if ( %$rref ) { #-- skip reference sequence or set atts from hash if ( !exists ($rref->{$idR}) ) { next; } else { ($refoff, $reflen, $refdir) = @{$rref->{$idR}}; } @@ -988,7 +988,7 @@ ($refoff, $reflen, $refdir) = (0, $lenR, 1); } - if ( defined (%$qref) ) { + if ( %$qref ) { #-- skip query sequence or set atts from hash if ( !exists ($qref->{$idQ}) ) { next; } else { ($qryoff, $qrylen, $qrydir) = @{$qref->{$idQ}}; } @@ -1031,7 +1031,7 @@ } - if ( !defined (%$rref) ) { + if ( !%$rref ) { if ( $ismultiref ) { print STDERR "WARNING: Multiple ref sequences overlaid, try -R or -r\n"; @@ -1041,7 +1041,7 @@ } } - if ( !defined (%$qref) ) { + if ( !%$qref ) { if ( $ismultiqry && !$OPT_coverage ) { print STDERR "WARNING: Multiple qry sequences overlaid, try -Q, -q or -c\n";